11-18-2009
Need help with extracting records from unix file
Hi,
Please help, Input file is on Linux box and the input file has data in just one line with 1699741696 characters.
Sample Input:
<xml><document coll="uspatfull" version="0"><CMSdoc>xxxantivirus <tag1>1</tag1></CMSdoc></document><document coll="uspatfull" version="0"><CMSdoc>yyy<tag1> a</tag1></CMSdoc></document>><document coll="uspatfull" version="0"><CMSdoc>likeavirusesxxx<tag1>aaa</tag1></CMSdoc></document></xml>
Output should be:
If data like "virus" appears anywhere between the document tags we need that in the output.
<xml><document coll="uspatfull" version="0"><CMSdoc>xxxantivirus <tag1>1</tag1></CMSdoc></document><document coll="uspatfull" version="0"><CMSdoc>likeavirusesxxx<tag1>aaa</tag1></CMSdoc></document></xml>
Thanks!
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LEARN ABOUT DEBIAN
g_h2order
g_h2order(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_h2order(1)
NAME
g_h2order - computes the orientation of water molecules
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_h2order -f traj.xtc -n index.ndx -nm index.ndx -s topol.tpr -o order.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w
-xvg enum -d string -sl int
DESCRIPTION
g_h2order computes the orientation of water molecules with respect to the normal of the box. The program determines the average cosine of
the angle between the dipole moment of water and an axis of the box. The box is divided in slices and the average orientation per slice is
printed. Each water molecule is assigned to a slice, per time frame, based on the position of the oxygen. When -nm is used, the angle
between the water dipole and the axis from the center of mass to the oxygen is calculated instead of the angle between the dipole and a box
axis.
FILES
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-n index.ndx Input
Index file
-nm index.ndx Input, Opt.
Index file
-s topol.tpr Input
Run input file: tpr tpb tpa
-o order.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 19
Set the nicelevel
-b time 0
First frame (ps) to read from trajectory
-e time 0
Last frame (ps) to read from trajectory
-dt time 0
Only use frame when t MOD dt = first time (ps)
-[no]wno
View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-d string Z
Take the normal on the membrane in direction X, Y or Z.
-sl int 0
Calculate order parameter as function of boxlength, dividing the box in nr slices.
KNOWN PROBLEMS
- The program assigns whole water molecules to a slice, based on the first atom of three in the index file group. It assumes an order
O,H,H. Name is not important, but the order is. If this demand is not met, assigning molecules to slices is different.
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_h2order(1)